OpSeF : Open Source Python Framework for Collaborative Instance Segmentation of Bioimages

Various pre-trained deep learning models for the segmentation of bioimages have been made available as developer-to-end-user solutions. They are optimized for ease of use and usually require neither knowledge of machine learning nor coding skills. However, individually testing these tools is tedious and success is uncertain. Here, we present the Open Segmentation Framework (OpSeF), a Python framework for deep learning-based instance segmentation. OpSeF aims at facilitating the collaboration of biomedical users with experienced image analysts. It builds on the analysts' knowledge in Python, machine learning, and workflow design to solve complex analysis tasks at any scale in a reproducible, well-documented way. OpSeF defines standard inputs and outputs, thereby facilitating modular workflow design and interoperability with other software. Users play an important role in problem definition, quality control, and manual refinement of results. OpSeF semi-automates preprocessing, convolutional neural network (CNN)-based segmentation in 2D or 3D, and postprocessing. It facilitates benchmarking of multiple models in parallel. OpSeF streamlines the optimization of parameters for pre- and postprocessing such, that an available model may frequently be used without retraining. Even if sufficiently good results are not achievable with this approach, intermediate results can inform the analysts in the selection of the most promising CNN-architecture in which the biomedical user might invest the effort of manually labeling training data. We provide Jupyter notebooks that document sample workflows based on various image collections. Analysts may find these notebooks useful to illustrate common segmentation challenges, as they prepare the advanced user for gradually taking over some of their tasks and completing their projects independently. The notebooks may also be used to explore the analysis options available within OpSeF in an interactive way and to document and share final workflows. Currently, three mechanistically distinct CNN-based segmentation methods, the U-Net implementation used in Cellprofiler 3.0, StarDist, and Cellpose have been integrated within OpSeF. The addition of new networks requires little; the addition of new models requires no coding skills. Thus, OpSeF might soon become both an interactive model repository, in which pre-trained models might be shared, evaluated, and reused with ease.Peer reviewe

Ounjougou (Mali): A history of holocene settlement at the southern edge of the Sahara

The area of Ounjougou consists of a series of gullies cut through Upper Pleistocene and Holocene formations on the Dogon Plateau in the Sahel at the south edge of the Sahara Desert. Here the authors have chronicled a stratified sequence of human occupation from the tenth to the second millennium BC, recording natural and anthropogenic strata containing artefacts and micro- and macro- palaeoecological remains, mostly in an excellent state of preservation. They present a first synthesis of the archaeological and environmental sequence for the Holocene period, define five main occupation phases for Ounjougou, and attempt to place them within the context of West African prehistor

Climate change mitigation potential of biochar from forestry residues under boreal condition

Forest harvest residue is a low-competitive biomass feedstock that is usually left to decay on site after forestry operations. Its removal and pyrolytic conversion to biochar is seen as an opportunity to reduce terrestrial CO2 emissions and mitigate climate change. The mitigation effect of biochar is, however, ultimately dependent on the availability of the biomass feedstock, thus CO2 removal of biochar needs to be assessed in relation to the capacity to supply biochar systems with biomass feedstocks over prolonged time scales, relevant for climate mitigation. In the present study we used an assembly of empirical models to forecast the effects of harvest residue removal on soil C storage and the technical capacity of biochar to mitigate national-scale emissions over the century, using Norway as a case study for boreal conditions. We estimate the mitigation potential to vary between 0.41 and 0.78 Tg CO2 equivalents yr−1, of which 79% could be attributed to increased soil C stock, and 21% to the coproduction of bioenergy. These values correspond to 9–17% of the emissions of the Norwegian agricultural sector and to 0.8–1.5% of the total national emission. This illustrates that deployment of biochar from forest harvest residues in countries with a large forestry sector, relative to economy and population size, is likely to have a relatively small contribution to national emission reduction targets but may have a large effect on agricultural emission and commitments. Strategies for biochar deployment need to consider that biochar's mitigation effect is limited by the feedstock supply which needs to be critically assessed.acceptedVersio

The emergence of pottery in Africa during the tenth millennium cal BC: new evidence from Ounjougou (Mali)

New excavations in ravines at Ounjougou in Mali have brought to light a lithic and ceramic assemblage that dates from before 9400 cal BC. The authors show that this first use of pottery coincides with a warm wet period in the Sahara. As in East Asia, where very early ceramics are also known, the pottery and small bifacial arrowheads were the components of a new subsistence strategy exploiting an ecology associated with abundant wild grasses. In Africa, however, the seeds were probably boiled (then as now) rather than made into brea

In vivo Imaging of Intact Drosophila Larvae at Sub-cellular Resolution

Recent improvements in optical imaging, genetically encoded fluorophores and genetic tools allowing efficient establishment of desired transgenic animal lines have enabled biological processes to be studied in the context of a living, and in some instances even behaving, organism. In this protocol we will describe how to anesthetize intact Drosophila larvae, using the volatile anesthetic desflurane, to follow the development and plasticity of synaptic populations at sub-cellular resolution1-3. While other useful methods to anesthetize Drosophila melanogaster larvae have been previously described4,5,6,7,8, the protocol presented herein demonstrates significant improvements due to the following combined key features: (1) A very high degree of anesthetization; even the heart beat is arrested allowing for lateral resolution of up to 150 nm1, (2) a high survival rate of > 90% per anesthetization cycle, permitting the recording of more than five time-points over a period of hours to days2 and (3) a high sensitivity enabling us in 2 instances to study the dynamics of proteins expressed at physiological levels. In detail, we were able to visualize the postsynaptic glutamate receptor subunit GluR-IIA expressed via the endogenous promoter1 in stable transgenic lines and the exon trap line FasII-GFP1. (4) In contrast to other methods4,7 the larvae can be imaged not only alive, but also intact (i.e. non-dissected) allowing observation to occur over a number of days1. The accompanying video details the function of individual parts of the in vivo imaging chamber2,3, the correct mounting of the larvae, the anesthetization procedure, how to re-identify specific positions within a larva and the safe removal of the larvae from the imaging chamber

The emergence of pottery in Africa during the tenth millennium cal BC: new evidence from Ounjougou (Mali)

New excavations in ravines at Ounjougou in Mali have brought to light a lithic and ceramic assemblage that dates from before 9400 cal BC. The authors show that this first use of pottery coincides with a warm wet period in the Sahara. As in East Asia, where very early ceramics are also known, the pottery and small bifacial arrowheads were the components of a new subsistence strategy exploiting an ecology associated with abundant wild grasses. In Africa, however, the seeds were probably boiled (then as now) rather than made into bread

Rich Counter-Examples for Temporal-Epistemic Logic Model Checking

Model checking verifies that a model of a system satisfies a given property, and otherwise produces a counter-example explaining the violation. The verified properties are formally expressed in temporal logics. Some temporal logics, such as CTL, are branching: they allow to express facts about the whole computation tree of the model, rather than on each single linear computation. This branching aspect is even more critical when dealing with multi-modal logics, i.e. logics expressing facts about systems with several transition relations. A prominent example is CTLK, a logic that reasons about temporal and epistemic properties of multi-agent systems. In general, model checkers produce linear counter-examples for failed properties, composed of a single computation path of the model. But some branching properties are only poorly and partially explained by a linear counter-example. This paper proposes richer counter-example structures called tree-like annotated counter-examples (TLACEs), for properties in Action-Restricted CTL (ARCTL), an extension of CTL quantifying paths restricted in terms of actions labeling transitions of the model. These counter-examples have a branching structure that supports more complete description of property violations. Elements of these counter-examples are annotated with parts of the property to give a better understanding of their structure. Visualization and browsing of these richer counter-examples become a critical issue, as the number of branches and states can grow exponentially for deeply-nested properties. This paper formally defines the structure of TLACEs, characterizes adequate counter-examples w.r.t. models and failed properties, and gives a generation algorithm for ARCTL properties. It also illustrates the approach with examples in CTLK, using a reduction of CTLK to ARCTL. The proposed approach has been implemented, first by extending the NuSMV model checker to generate and export branching counter-examples, secondly by providing an interactive graphical interface to visualize and browse them.Comment: In Proceedings IWIGP 2012, arXiv:1202.422

The Ig cell adhesion molecule Basigin controls compartmentalization and vesicle release at Drosophila melanogaster synapses

Synapses can undergo rapid changes in size as well as in their vesicle release function during both plasticity processes and development. This fundamental property of neuronal cells requires the coordinated rearrangement of synaptic membranes and their associated cytoskeleton, yet remarkably little is known of how this coupling is achieved. In a GFP exon-trap screen, we identified Drosophila melanogaster Basigin (Bsg) as an immunoglobulin domain-containing transmembrane protein accumulating at periactive zones of neuromuscular junctions. Bsg is required pre- and postsynaptically to restrict synaptic bouton size, its juxtamembrane cytoplasmic residues being important for that function. Bsg controls different aspects of synaptic structure, including distribution of synaptic vesicles and organization of the presynaptic cortical actin cytoskeleton. Strikingly, bsg function is also required specifically within the presynaptic terminal to inhibit nonsynchronized evoked vesicle release. We thus propose that Bsg is part of a transsynaptic complex regulating synaptic compartmentalization and strength, and coordinating plasma membrane and cortical organization

N-methyl-β-carboline alkaloids: structure-dependent photosensitizing properties and localization in subcellular domains

N-methyl-Beta-carboline (bC) alkaloids, including normelinonine F and melinonine F, have been found in a vast range of living species playing different biological, biomedical and/or pharmacological roles. Despite this, molecular bases of the mechanisms through which these alkaloids would exert their effect still remain unknown. Fundamental aspects including the photosensitizing properties and intracellular internalization of a selected group of N-methyl-bC alkaloids were investigated herein. Data reveal that methylation of the bC main ring enhances its photosensitizing properties either by increasing its binding affinity with DNA as biomolecular target and/or by increasing its oxidation potential, in a structure dependent manner. As a general rule, N(9)-substituted bCs showed the highest photosensitizing efficiency. With the exception of 2-methyl-harminium, all the N-methyl-bCs investigated herein induce a similar DNA photodamage profile, dominated largely by oxidized purines. This fact represents a distinctive behavior when comparing with N-unsubstituted-bCs. On the other hand, although all the investigated compounds might accumulate mainly into the mitochondria of HeLa cells, methylation provides a distinctive dynamic pattern for mitochondrial uptake. While rapid (passive) diffusion is most probably reponsible for the prompt uptake/release of neutral bCs, an active transport appears to mediate the (reatively slow) uptake of the quaternary cationic bCs. This might be a consequence of a distinctive subcellular localization (mitochondrial membrane and/or matrix) or interaction with intracellular components. Biomedical and biotechnological implications are also discussed herein.Fil: Denofrio, Maria Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); ArgentinaFil: Rasse Suriani, Federico Ariel Osvaldo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas; ArgentinaFil: Paredes, Jose M.. Universidad de Granada. Facultad de Farmacia. Departamento de Fisicoquimica.; EspañaFil: Fassetta, Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); ArgentinaFil: Crovetto, Luis. Universidad de Granada. Facultad de Farmacia. Departamento de Fisicoquimica.; EspañaFil: Giron, Maria D.. Universidad de Granada. Facultad de Farmacia.; EspañaFil: Salto, Rafael. Universidad de Granada. Facultad de Farmacia.; EspañaFil: Epe, Bernd. Johannes Gutenberg Universitat Mainz; AlemaniaFil: Cabrerizo, Franco Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentin